GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas putida KT2440

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate PP_4716 PP_4716 Phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Putida:PP_4716
          Length = 446

 Score =  206 bits (523), Expect = 2e-57
 Identities = 157/460 (34%), Positives = 238/460 (51%), Gaps = 30/460 (6%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG   E  ITP+F LK+G A G   +++G  R  V+VG+DTR+SG M + AL
Sbjct: 4   KYFGTDGIRGRVGEYPITPDFMLKLGWAAGMAFRKQGHCR--VLVGKDTRISGYMFESAL 61

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G DV+ +G  PTPAI + T  F+A+ G VI+ASHNP + NGIK     G  L 
Sbjct: 62  EAGLSAAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGQGTKLP 121

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRV----DVEAIKKRRPF 176
            E E ++EEL   +     +  ++G++ R  D    YIE  K+ V      E +K     
Sbjct: 122 DEVELMIEEL-LDQPMTVVESGKLGKVSRINDAAGRYIEFCKSSVPSSTSFEGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236
           +VVD ++GA     P + RELG  V  ++A PDG     N      +++     V    A
Sbjct: 176 LVVDCAHGATYKVAPSVFRELGADVTVLHAQPDG--LNINEGCGSTHIESLQAAVLVGHA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG---GGLLVTTIATSNLLDD 293
           D G+A DGD DR + +D  G  + GD+   ++A   L+E+G   GG++ T +  SNL  +
Sbjct: 234 DLGIAFDGDGDRVLMVDHTGAIVDGDELLFIIA-RDLQEHGKLQGGVVGTLM--SNLGLE 290

Query: 294 IAKRN-GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEI 352
           +A ++     +R KVGD  V   LLE    +GGE +G V+  +     D  +   +++  
Sbjct: 291 LALKDLDIPFVRAKVGDRYVMAELLEREWLVGGENSGHVVCCNHTTTGDAIIAALQVLMA 350

Query: 353 FAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFD 412
             + G+  ++    L K  Q      V  + +   +KV  L E    K  +   T+ +  
Sbjct: 351 LKRRGETLAQARQALRKCPQ------VLINVRFGASKVDPL-EHPAVKEASAKVTEALAG 403

Query: 413 DGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452
            G VL+R SGTEP++R+  E + E + R + E   KL+ E
Sbjct: 404 RGRVLLRKSGTEPLVRVMVEGEDESQVRAHAEALAKLVGE 443


Lambda     K      H
   0.317    0.139    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 515
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 456
Length of database: 446
Length adjustment: 33
Effective length of query: 423
Effective length of database: 413
Effective search space:   174699
Effective search space used:   174699
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory